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peak picking

Piotr Klukowski, Michal Augoff, Maciej Zieba, Maciej Drwal, Adam Gonczarek, Michal J Walczak
Motivation: Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy...
March 14, 2018: Bioinformatics
Charlie Beirnaert, Pieter Meysman, Trung Nghia Vu, Nina Hermans, Sandra Apers, Luc Pieters, Adrian Covaci, Kris Laukens
Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction...
March 1, 2018: PLoS Computational Biology
Jinru Liang, Wenji Sun
A mass spectrometry guided elution-extrusion counter-current chromatography protocol was developed to separate chemical components from Cornus officinalis Sieb. et Zucc. Ion current extraction, a mass spectrometry based data post-acquisition method, was utilized to boost the separation power and scope of counter-current chromatography technique in this study. As a peak re-picking and denoising tool, ion current extraction was carried out to process the liquid chromatography with mass spectrometry and the counter-current chromatography with mass spectrometry data...
February 14, 2018: Journal of Separation Science
Marko Kosicek, Ivan Gudelj, Anita Horvatic, Tanja Jovic, Frano Vuckovic, Gordan Lauc, Silva Hecimovic
Increasing evidence implicates lysosomal dysfunction in the pathogenesis of neurodegenerative diseases, including the rare inherited lysosomal storage disorders (LSDs) and the most common neurodegenerative diseases, such as Alzheimer's and Parkinson's disease (AD and PD). While the triggers of the lysosomal impairment may involve the accumulated macromolecules or dysfunction of the lysosomal enzymes, the role of the lysosomal glycocalyx in the lysosomal (dys)function has not been studied. The goal of this work was to analyze whether there are changes in the lysosomal glycocalyx in a cellular model of a LSD Niemann-Pick type C disease (NPC)...
January 24, 2018: Molecular & Cellular Proteomics: MCP
Pierre-Frederic Villard, Peter E Hammer, Douglas P Perrin, Pedro J Del Nido, Robert D Howe
BACKGROUND: Common surgical procedures on the mitral valve of the heart include modifications to the chordae tendineae. Such interventions are used when there is extensive leaflet prolapse caused by chordae rupture or elongation. Understanding the role of individual chordae tendineae before operating could be helpful to predict whether the mitral valve will be competent at peak systole. Biomechanical modelling and simulation can achieve this goal. METHODS: We present a method to semi-automatically build a computational model of a mitral valve from micro CT (computed tomography) scans: after manually picking chordae fiducial points, the leaflets are segmented and the boundary conditions as well as the loading conditions are automatically defined...
January 22, 2018: International Journal of Medical Robotics + Computer Assisted Surgery: MRCAS
Ruo-Mi Guo, Qing-Ling Li, Zhong-Xing Luo, Wen Tang, Ju Jiao, Jin Wang, Zhuang Kang, Shao-Qiong Chen, Yong Zhang
Objective: To noninvasively assess the neurodegenerative changes in the brain of patients with Niemann-Pick type C (NPC) disease by measuring the lesion tissue with the iterative decomposition of water and fat with echo asymmetry and least square estimation-iron quantification (IDEAL-IQ). Materials and Methods: Routine brain MRI, IDEAL-IQ and 1H-proton magnetic resonance spectroscopy (1H-MRS, served as control) were performed on 12 patients with type C Niemann-Pick disease (4 males and 8 females; age range, 15-61 years; mean age, 36 years) and 20 healthy subjects (10 males and 10 females; age range, 20-65 years; mean age, 38 years)...
January 2018: Korean Journal of Radiology: Official Journal of the Korean Radiological Society
Angélique Goffin, Sabrina Guérin, Vincent Rocher, Gilles Varrault
The online monitoring of dissolved organic matter (DOM) in raw sewage water is expected to better control wastewater treatment processes. Fluorescence spectroscopy offers one possibility for both the online and real-time monitoring of DOM, especially as regards the DOM biodegradability assessment. In this study, three-dimensional fluorescence spectroscopy combined with a parallel factor analysis (PARAFAC) has been investigated as a predictive tool of the soluble biological oxygen demand in 5 days (BOD5) for raw sewage water...
January 11, 2018: Environmental Science and Pollution Research International
C Stremmel, R Schuchert, F Wagner, R Thaler, T Weinberger, R Pick, E Mass, H C Ishikawa-Ankerhold, A Margraf, S Hutter, R Vagnozzi, S Klapproth, J Frampton, S Yona, C Scheiermann, J D Molkentin, U Jeschke, M Moser, M Sperandio, S Massberg, F Geissmann, C Schulz
Tissue macrophages in many adult organs originate from yolk sac (YS) progenitors, which invade the developing embryo and persist by means of local self-renewal. However, the route and characteristics of YS macrophage trafficking during embryogenesis are incompletely understood. Here we show the early migration dynamics of YS-derived macrophage progenitors in vivo using fate mapping and intravital microscopy. From embryonic day 8.5 (E8.5) CX3CR1+ pre-macrophages are present in the mouse YS where they rapidly proliferate and gain access to the bloodstream to migrate towards the embryo...
January 8, 2018: Nature Communications
Henrik Tünnermann, Akira Shirakawa
Ultrafast fiber amplifiers are usually limited in terms of pulse energy and peak power due to fiber damage and nonlinearities. On the other hand, fiber amplifiers are very energy efficient. To take advantage of this efficiency, but still scale the pulse energy, coherent combining and pulse stacking have become the method of choice. Here we show how to directly and symmetrically stack up the pulses from an oscillator chain, using delay lines and phase preshaping of a 48 MHz, 1.5 μm master oscillator. This method avoids the need for high-power low-loss dumpers as in passive stack and dump cavities and, compared to divided pulse amplification (DPA), it eliminates the need for splitting pulses and pulse picking and, thus, optimally utilizes the available seed power...
December 1, 2017: Optics Letters
James Blundell, Steven Frisson, Anupam Chakrapani, Paul Gissen, Chris Hendriksz, Suresh Vijay, Andrew Olson
Niemann-Pick type C (NP-C) is a rare recessive disorder associated with progressive supranuclear gaze palsy. Degeneration occurs initially for vertical saccades and later for horizontal saccades. There are studies of oculomotor degeneration in adult NP-C patients [1, 2] but no comparable studies in children. We used high-resolution video-based eye tracking to record monocular vertical and horizontal eye movements in 2 neurological NP-C patients (children with clinically observable oculomotor abnormalities) and 3 pre-neurological NP-C patients (children without clinically observable oculomotor abnormalities)...
February 2018: Molecular Genetics and Metabolism
Christian D Kelstrup, Dorte B Bekker-Jensen, Tabiwang N Arrey, Alexander Hogrebe, Alexander Harder, Jesper V Olsen
Progress in proteomics is mainly driven by advances in mass spectrometric (MS) technologies. Here we benchmarked the performance of the latest MS instrument in the benchtop Orbitrap series, the Q Exactive HF-X, against its predecessor for proteomics applications. A new peak-picking algorithm, a brighter ion source, and optimized ion transfers enable productive MS/MS acquisition above 40 Hz at 7500 resolution. The hardware and software improvements collectively resulted in improved peptide and protein identifications across all comparable conditions, with an increase of up to 50 percent at short LC-MS gradients, yielding identification rates of more than 1000 unique peptides per minute...
January 5, 2018: Journal of Proteome Research
Luz Patricia Hernandez, Dominique Adriaens, Christopher H Martin, Peter C Wainwright, Bert Masschaele, Manuel Dierick
Dietary partitioning often accompanies the increased morphological diversity seen during adaptive radiations within aquatic systems. While such niche partitioning would be expected in older radiations, it is unclear how significant morphological divergence occurs within a shorter time period. Here we show how differential growth in key elements of the feeding mechanism can bring about pronounced functional differences among closely related species. An incredibly young adaptive radiation of three Cyprinodon species residing within hypersaline lakes in San Salvador Island, Bahamas, has recently been described...
November 21, 2017: Journal of Anatomy
Laure Margueritte, Petar Markov, Lionel Chiron, Jean-Philippe Starck, Catherine Vonthron-Sã nà Cheau, Mã Lanie Bourjot, Marc-Andrà Delsuc
Liquid state NMR is a powerful tool for the analysis of complex mixtures of unknown molecules. This capacity has been used in many analytical approaches: metabolomics, identification of active compounds in natural extracts, characterization of species, and such studies require the acquisition of many diverse NMR measurements on series of samples. While acquisition can easily be performed automatically, the number of NMR experiments involved in these studies increases very rapidly and this data avalanche requires to resort to automatic processing and analysis...
November 20, 2017: Magnetic Resonance in Chemistry: MRC
Luis F Aristizábal, Melissa Johnson, Suzanne Shriner, Robert Hollingsworth, Nicholas C Manoukis, Roxana Myers, Paul Bayman, Steven P Arthurs
The coffee berry borer (CBB), Hypothenemus hampei, is the most significant insect pest of coffee worldwide. Since CBB was detected in Puerto Rico in 2007 and Hawaii in 2010, coffee growers from these islands are facing increased costs, reduced coffee quality, and increased pest management challenges. Here, we outline the CBB situation, and summarize the findings of growers, researchers, and extension professionals working with CBB in Hawaii. Recommendations for the Integrated Pest Management (IPM) program for CBB in Hawaiian Islands and Puerto Rico include: (1) establish a CBB monitoring program, (2) synchronize applications of insecticides with peak flight activity of CBB especially during the early coffee season, (3) conduct efficient strip-picking as soon as possible after harvest and perform pre-harvest sanitation picks in CBB hotspots if needed, (4) establish protocols to prevent the escape of CBB from processing areas and when transporting berries during harvest, and (5) stump prune by blocks...
November 14, 2017: Insects
Antonella Ferrante, Antonella Pezzola, Andrea Matteucci, Antonella Di Biase, Lucilla Attorri, Monica Armida, Alberto Martire, Yijuang Chern, Patrizia Popoli
Niemann-Pick C is a fatal neurovisceral disorder caused, in 95% of cases, by mutation of NPC1 gene. Therapeutic options are extremely limited and new "druggable" targets are highly warranted. We previously demonstrated that the stimulation of the adenosine A2A receptor (A2A R) normalized the pathological phenotype of cellular models of NPC1. Since the validation of A2A Rs as a therapeutic target for NPC1 can be obtained only conducting studies in in vivo models of the disease, in the present paper, the effects of two agonists of A2A Rs were evaluated in the mouse model Balb/c Npc1nih , hereafter indicated as NPC1-/-...
February 2018: Neurobiology of Disease
Markus Niklasson, Renee Otten, Alexandra Ahlner, Cecilia Andresen, Judith Schlagnitweit, Katja Petzold, Patrik Lundström
NMR spectroscopy is uniquely suited for atomic resolution studies of biomolecules such as proteins, nucleic acids and metabolites, since detailed information on structure and dynamics are encoded in positions and line shapes of peaks in NMR spectra. Unfortunately, accurate determination of these parameters is often complicated and time consuming, in part due to the need for different software at the various analysis steps and for validating the results. Here, we present an integrated, cross-platform and open-source software that is significantly more versatile than the typical line shape fitting application...
October 2017: Journal of Biomolecular NMR
Xavier Domingo-Almenara, J Rafael Montenegro-Burke, H Paul Benton, Gary Siuzdak
No abstract text is available yet for this article.
November 3, 2017: Analytical Chemistry
Ayoub Baali, Hajar Bourassi, Samira Falah, Wahbi Abderrazik, Khalid Manchih, Khadija Amenzoui, Ahmed Yahyaoui
BACKGROUND AND OBJECTIVE: Sardinella sp. has gained much attention lately because of its biomass increase, which might be the result of climatic changes occurring across the Atlantic sea. Little information is known about reproduction of these species particularly in the Moroccan Atlantic area. The objective of the this study was to explore some aspects of the reproductive biology of Sardinella in the South of Atlantic Moroccan coast. MATERIALS AND METHODS: Monthly samples were collected during the period between February, 2015 and January, 2016 in the area between Cape Boujdor and Cape Blanc...
2017: Pakistan Journal of Biological Sciences: PJBS
Jingshu Guo, Peter W Villalta, Robert J Turesky
Long-term exposures to environmental toxicants and endogenous electrophiles are causative factors for human diseases including cancer. DNA adducts reflect the internal exposure to genotoxicants and can serve as biomarkers for risk assessment. Liquid chromatography-multistage mass spectrometry (LC-MSn ) is the most common method for biomonitoring DNA adducts, generally targeting single exposures and measuring up to several adducts. However, the data often provide limited evidence for a role of a chemical in the etiology of cancer...
November 7, 2017: Analytical Chemistry
Eric T Dziekonski, Joshua T Johnson, Kenneth W Lee, Scott A McLuckey
An electrostatic linear ion trap (ELIT) has been configured to allow for the simultaneous acquisition of mass spectra via Fourier transform (FT) techniques (frequency measurement) and via time-of-flight (TOF; time measurement). In the former case, the time-domain image charge derived from a pick-up electrode in the field-free region of the ELIT is converted to frequency-domain data via Fourier transformation (i.e., FT-ELIT MS). In the latter case, the time difference between ion injection into the ELIT and ion detection after release from the ELIT using a microchannel plate (MCP) enables the acquisition of multireflection time-of-flight mass spectra (MR-TOF MS)...
October 17, 2017: Analytical Chemistry
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